Halo: The Final Struggle
by PcA
Summary: After Halo was destroyed, Master Chief set to journey back to Earth, confident on his abilities. What he will find is a world tear apart by change. Is it John's true destiny to activate Halo? Will he accept it? (NEW! Chapter 2. Reviews are welcomed.)
1. Touched By An Angel

- Chapter I -

**_Touched By An Angel_**

In a deep, vast region of space, just outside the Solar System's meteor belt… the silence and tranquillity was ripped apart for a second, as a single Longsword Ship cruised the eternal silence, one of the smaller ships of the UNSC armada. Aboard the ship was a lone soldier, lying down in his chair, as though as resting after passing through dire trials, last surviving SPARTAN-II, John-117, known to most by the title of Master Chief. In front of him, over the ship's main computer, eyes shut with concentration was former Pillar of Autumn's AI, Cortana. 

It had been seven years since this small ship had taken on a long and lonely journey through space, after they both escaped from Halo and eradicated both the threat of the Flood and the threat of 343 Guilty Spark, who Cortana almost failed to stop from destroying the galaxy. Because Halo wasn't, as they both learned, a simple artificial planet. Having been built by the Forerunners, it was a fortress world designed to contain the flood. More so, it had been designed with the means to, in conjunction with other Halo rings across the galaxy, wipe the galaxy clean of all sentient life, as a means to starve the flood to death. Even after destroying Halo and seemingly avoid both the threat of the flood and of Guilty Spark, Chief was restless. He knew that the Covenant threat was still present, and that it was quite possible that, despite Keyes' efforts, the Covenant might still have found Earth's location after the assault on Reach. 

As this thoughts dwelled in his mind, Cortana finally opened her eyes, and spoke with a tone of rather deception on her voice. "Well, I'm not sure what to figure out of this Index thing. It's written in a code I can only partially decipher, and that portion I can makes absolutely no sense". 

John rolled his eyes inside his helmet, taking little notice on her words. "Hey, are you even listening to me?", Cortana added, sounding annoyed, "You don't realise the importance of this, do you? This "Index" is the key to activating the Halo rings!".    "So?", replied John. "Halo is destroyed, as you should remember, our objective now is to get to Earth. The covenant remain a serious threat. There is no need to worry about those things anymore." 

Cortana, looking rather angry and exasperated at those words, "Have you forgot that we only destroyed ONE of the Halos? Plus, chances are that floating annoying little thin-…Guilty Spark has escaped and is now on it's way to activate the other  Halos".. "which, and by the Monitor's words, are hundreds of light-years away from each other.", finished John.

"Oh, I don't know how you humans were able to create AI beings in the first place." Sighed Cortana, before disappearing again into bits of code, probably to study the Index more clearly.

"We will be reaching Earth in a few hours time, so do try to get some rest, you'll probably need it", echoed a voice through the ship's communication speakers, "after all, ONI will be no less than interested after they about our little escapade, and – whoa, Chief? We're receiving some transmission here."

John quickly got to his feet at those words and hurried to check on the ship's radar system. "Jammed.. who trying to communicate? What are they saying?"

"It's all very messy, wait a second, I'll put it on loud speak." As she did, a loud noise echoed through the ship, a strong female voice could be heard through all the interference, practically shouting so as to be heard through:

"IDENTIFY YOURSELF AT ONCE! THIS IS HALCYON WARSHIP AVENGING ANGEL'S CAPTAIN KREYSHA SPEAKING! ANY UNSC PERSONEL RESPOND! WHY ARE YOU IN RESTRICTED AREA? IDENTIFY YOURSELF OR WE WILL OPEN FIRE!"

"Looks as though as they mean business", commented Chief quietly, "Cortana, maybe we should let them know we're friends, just in case they decide to turn us into galactic dust?"

"One step ahead of you, as usual" replied Cortana, once again her purple translucent hologram self, smiling "this is a fortunate meeting, maybe this ship can take us to Earth… even though that message was quite obscure...". Before she could finish her line of thought, Kreysha's voice echoed once again, this time more clearly and calm:

"Welcome back Master Chief, we thought all crew of the Pillar of Autumn had been lost after the fall on Reach. I am sorry for the way we approached your ship, but it isn't normal to see one cruising this space these days that we do not know of. Nonetheless, t is most fortunate that we find you, your help will be of most importance considering… recent events. But you shall be informed fully once we reach Mars Command Central, we're pulling your ship towards the Avenging Angel at once."

No sooner after she finished that sentence, Chief felt a slight tremor rushing through the ship as it began heading towards the Avenging Angel's dock bays. Looking through his ship's cockpit, Chief saw the Avenging Angel for the first time. It was similar to the Pillar of Autumn, the last Halcyon-class ship he had travelled on, except this one looked slightly bulkier and even more heavily-armed. What was so surprising about the Avenging Angel that put him in charge of patrolling that area of space was that is was one of the first ships of the CP-1 line, which meant it's primary guns were equipped with Plasma capability, much like the standard Covenant cruiser. Cortana was surprised at this fact, when she pointed that out to John, "Chief, look… this ship is equipped with plasma weapons… how much can have things changed since…since Reach was destroyed?"

"From the looks of it, more than we can imagine", simply put John in is usually calm voice, even thought he was now more restless than ever before, and had the feeling much bad might have happened during their absence.  But he was spared the chance to think about it much, because the ship was finally landing inside the Avenging Angel's dock.

"Ok, let's go, Cortana. Ready?"

"I'll miss being in a ship.. _again_.", sighed Cortana before disappearing. John pulled her chip out of the ship's main computer, inserted him into his helmet socket and headed out to the exit.

The cargo bay was very dark and dusty, with only a flicker of light seen from the Avenging Angel filtered through the bay's doors. Strangely, Chief felt that old familiar feeling of being watched closely. After all, he had not went down there since the ship departed... "But no," he thought, shaking his head "nobody entered this ship besides me, it would have been impossible."

Just as he put those feelings aside, he caught the green flicker of  a plasma pistol, and dropped to the ground just in time to dodge the plasma bolt. 

"Chief, to your right!" Shouted Cortana, just as John quickly got up to his feet and withdrew his Assault Rifle. When he lighted up his flashlight, he saw that the bay was filled with crates of various sizes. The mysterious attacker was gone.

"I thought you said no one survived", John asked Cortana, with only the slightest trace of annoyance in his tone.

"It doesn't make any sense… unless it was already inside the ship…but what could it be? A Covenant? Or maybe…","Shh. There will be time to talk later." Advised John, as he moved quietly through the crates. But there was no one to be seen. And then it happened. In less than a second, John felt a painful stinging feeling in his neck, as some low horrid inhuman grunts filled his ear. His smell was like that of a rotten corpse. It was a flood, and it had caught Chief off his guard and manage to get through a weak spot in the seemingly impenetrable MJOLNIR armour. But then suddenly, in the midst of his pain Chief saw light flooding the docking bay and hear several shots being fired in his direction. He felt the pain stop, the flood knocked dead on the ship's floor, heavily disfigured by the shot impacts on the soft body.

"CHIEF! Are you ok? It was.. how come…a flood.. and it.. managed to penetrate your battle suit…", said Cortana in a small voice, sounding as surprised as Chief, but couldn't finish her sentence.

Still rather stunned by the pain, John turned to the docking doors and saw, against the light of the Avenging Angel's docking bay, a group of Marines, lead by one just a few inches smaller than the rest. But what made her different was the armour she wore. Chief thought it was strangely familiar…like the one he wore, but different at the same time… but it couldn't be.

"Is that…MJOLNIR armour?" Cortana spoke slowly, as though as her eyes were deceiving her. "But, only…those like you can…wear them."

The mysterious woman removed her helmet, revealing a long wave of black her. As it made continence and then walked towards Chief she talked:

"We're sorry we took care of your little stowaway, but it looks as though as you weren't friends anyway. Welcome, Master Chief. I'm S-III Captain Kreysha-121 of the Avenging Angel."

*

Next Chapter will include:

A strange dream? A journey to Earth? A meeting with old 'friends'? A space action  scene? All that and more in the next lengthier-than-the-first-chapter chapter 2 APOCALYPSE CAME YESTERDAY.


	2. “I Work Alone, Reduces Risk Of Friendly ...

- Chapter II -

**_"I Work Alone, Reduces Risk Of Friendly Fire To Zero"_**

"We never knew the whole story of the fall of Reach, but there were records of the Halcyon-class ship called 'Pillar of Autumn' entering the Slipstream with unknown coordinates, containing the last SPARTAN-II John 117. Your return is most unexpected.", stated Kreysha to Chief. They were in the medical ward of the Angel, and Chief's suit was being quickly repaired, after the injury was taken care of, by a small buzzing droid which looked much like a spider, should a spider be capable of repairing electronic devices.

"I've never seen anything that could do this to a MJOLNIR amour, except for the Covenant's fuel rod guns, perhaps. But to see it done by a melee attack..", stated the ward-master, a young man called Hermes. "What kind of creature was that? We've sent it into the containment area, it will be further studied at Mars, but I've never seen anything like it..."

"They're called the Flood, I've met them during our.. time out. I won't say more about it but to the right persons." John said, "But make sure it stays on quarantine; they're extremely dangerous.. even for a SPARTAN, it seems", he finished, with a small touch of bitterness in his voice. In his mind, Chief couldn't explain to himself how could a single flood have bested him. Had long the journey Earth dimmed his strength? Or was it something else, something he couldn't explain?

Cortana, who had been placed in a portable holographic panel, was staring, slightly perplexed, at the droid's capabilities. "MJOLNIR armour are experimental, very hard to craft.. how can a mere droid be able to repair them?", she asked Kreysha.

"Technology has ramped up considerably since your disappearance, ma'am…sir. MJOLNIR armour has become much more common these days. Necessity called for it, unfortunately", Hermes finished with a sigh and stared through the ward's windows into space.

"So the continuity of the SPARTAN project was a 'necessity' as well?", John asked, as he got up fully recovered, staring at the repaired portion of his suit, which now looked as good as new.

"Yes.", merely replied Kreysha. "But as I stated before, I am not the one to talk about such matters. Don't worry, you shall have your questions answered soon enough."

"But where are we headed to? Earth?", asked Cortana.

"Earth… no, AI, we are headed towards Mars, ONI's and UNSC's new Command Centre, again because of necessity." Kreysha replied as though as the reference to Earth was painful to her.

Chief, taking note the tone of her voice. "So the Covenant have arrived… and I came too late", he said, drops of sweat coming down his forehead, although only he could take notice of it. Kreysha merely nodded. Cortana looked blankly at her.

"But.. how come..", she started, but Kreysha stopped her.

"Not here, not now, AI." As she headed towards the door she added to Chief, "Stay here until we arrive, your strength will be needed, and certainly the commanders will wish to speak to you. For some reason, your disappearance caused much uproar among ONI. Searches were actually conducted for the Pillar of Autumn, but necessity saw to it that the entire fleet was recalled to Earth." With that, she left.

"I'll leave you alone as well sir. Rest well.", said Hermes before leaving for his room.

John and Cortana were left in the room, with many news to ponder on, the weight of all the changes that had come to the world they thought they knew so well overwhelming them.

"Well Chief, I'd reckon much has, indeed, changed since we left. But… what has happened to Earth? Could it have been…", Cortana spoke slowly, as though as the thought of it alone was unbearable.

"Destroyed?", Chief completed calmly. "No, I don't think it is. If my guess is correct, I'd say Earth is under siege even as we speak."

"What about that SPARTAN-III, Kreysha? And plasma weapons in human ships? This is all very confusing…"

"Well," said John, while removing his helmet and lying down in a small bunk, "I suggest we wait and see where we get thrown off to. But I think we'll have a chance to meet with some old 'friends' very soon."

Chief was walking down an ancient Forerunner facility. From the looks of it, no living being had set foot on it for hundreds of  thousands of years, and yet, he felt like we was walking down in a familiar place, like the adult who returns to the house he used to live in as a baby. In his left hand he held the Index, his right hand was free.      

He held no weapon, as though as there was no threat in that place that could compromise his mission.

Cortana's voice was shouting cries of pleading at his ears, saying "Don't do it Chief! Please!", but he did not care. Some greater voice was telling him, "Keep moving. That's what you were meant to do." He sensed he was getting close to his goal. His heart was thumping with anticipation.

"Chief! Sir? CHIEF!" 

John opened his eyes. He was lying down in the same bunk in the medical ward of the Avenging Angel he had fallen asleep in. The dream's details were fading away from his mind… he remembered walking in an old structure… holding something of great importance… he was going to, at last, fulfil his mission, the true purpose for which he was created... but that feeling was very pale now, like a distant memory sinking back to the depths of his mind.

"Sir, are you ok? Sorry to wake you up, but we're entering Mars atmosphere now, Captain Kreysha is waiting for you in the bridge, we better hurry up." As Chief raised his eyes, he saw that Hermes was leaning towards him, looking nervous. "You were trashing around and moaning in your sleep, is everything alright?"

"Yes, it's…nothing, just a dream." Said Chief with an unusually human tone to his voice. "Where is Cortana?", he asked, trying to regain his usually cold and calm voice.

"The AI accompanying you? Captain sent her ahead to Mars, she is already with in the Command Center. We should get to the bridge, sir. This way."

John followed Hermes out of the medical ward, still pondering about his strange dream. Little did he take notice on the muttering that went on through all the corridors as he passed. Some marines did cheer as he passed, while some did not recognize him at all. John did not care for either one of the groups. It was not his wish to be the regular hero. He just wanted to do what he could to destroy all threats to Humanity…that was the purpose for which he was raised, after all…

"Here's the bridge, sir. Captain's waiting for you…I should get back to the medical ward." 

"Uh..right, thanks", said Chief, as he woke up from his thoughts. He looked at the bridge. It brought back memories of the Pillar of Autumn. They were both similar, in a way, except that this bridge was actually much bigger than the other one, and had a circular force field cutting right through it. Kreysha was talking through the holo-panel at somebody, next to the ship's controls, though Chief couldn't see who it was, since that, incidentally or purposefully, Kreysha ended the conversation as he approached her. Chief looked through the ship's windows and saw Mars' red sky, filled with other Halcyon ships as well as a number of different ships.

"Chief..  I trust you rested well?" She asked.

"I've slept in worse places, thanks." Said Chief. Kreysha chuckled.

"We're just setting the gravity lift, we'll be able to descend to the surface soon." Kreysha pointed at the energy field circle in the center of the bridge. Several technicians were busy with the control  panels around it.

"Another advancement born out of necessity?" Chief asked, with irony.

"Yes. Too much time is lost in the landing and takeoff of ships. We learned - _the hard way_ – that often that's enough to tip off the balance of a battle."

"Ma'am! We're ready to go. Whenever you're ready!"

"Ok, let's go down Chief, we shouldn't keep anyone waiting."

"Whoever it is, has waited seven years, so a couple of minutes probably won't matter." Added John moodily.

"I trust you have used a gravity lift before?"

Chief's memories quickly turned to the Truth and  Reconciliation, the Covenant cruiser he had once boarded to rescue captain Keyes. The cruiser he boarded again to find Keyes dead.. assimilated by the flood… "Focus, damn it! It wasn't your fault, you did all you could." John reminded him, almost pleadingly.

"Yes, I have. But never used one to get _out_ of a ship", said Chief.

"Always a good time to try", replied Kreysha. "Alright we're ready, get us down!" She added to the technicians.

As they activated the teleported, it began shining with bright white energy, as opposed to the Covenant's purple. Once again he felt that feeling of being pulled by an invisible force. Only this time he was sinking down into a sea of red.  He saw the clouds whirling out of the way, he caught the shiny tops of several skyscrapers, although there were only a few when compared to Reach's ever-reaching cities of glittering sky-high buildings. The rest of the surface seemed as deserted as when man must set foot on it, save for a few military camps scattered and large roads rushing with convoys of troops and supplies: it was clearly a place where war was being prepared. Most of those military resources were being led off to Earth, only a few remaining to protect the leaders of the human race. But that vision disappeared right in front of John's eyes. He was being lowered into a very large structure, bigger than anyone else. He saw a variety of docking bays, housing  ships ranging from the smaller and the bigger of the UNSC armada during his descent. As he reached the bottom floor, he was surrounded by lush vegetation, kept there probably as a last living memory of Earth's once ever-reaching forests and jungles.

They had finally reached their destination. It was a large round room located in the middle of the vegetation, and seemed as clean and neat as though as people in that room had no knowledge of any conflict between Humans and Covenants. But that would be misinterpretation. The room was full of computers, more advanced than any ever created by mankind, and messages were being sent back and forth between there and every UNSC ship every second. It was the room where war was being played, like every ship was a pawn in a huge chess board with the galaxy as the backdrop.

Already waiting for Master Chief was Cortana, with a very serious look on her face, eyes shut as she examined the information on the main computer, which displayed a schematic of Earth, containing an unnatural large number of red dots on it, when compared to the number of yellow ones. That couldn't be good.

"Chief, are you ok?", asked Cortana, finally eyes opened.

"Yes. Thanks for waiting for me", replied Chief, slightly annoyed.

"I was ordered to come down early, sorry." 

 Standing by the computer were the single most important ONI and UNSC personnel. The people behind the war effort.

One of the men he recognized. Although old, there he was, standing straight and bold as ever.

"CPO Mendez?"

"That's Admiral Mendez for you, kid." Corrected the admiral, without concealing the smallest of  smiles.

The second man facing Chief was one he did not know, but he felt a great surge of respect towards him.

"Welcome, Master Chief. We are most happy about your return. We have much to discuss considering the current situation. I am Morgan Naxos, Commander of  all UNSC and ONI operations.", he spoke with a strong, determined voice. John could not help but to be remembered of Captain Keyes as he looked upon this man, leader of all men.

Looking at the third person, Chief recognized it as a woman. A woman Chief remembered, every single day, since the day he was taken from his parents and inserted into the project that altered is physical appearance, his way of thinking, even his DNA. 

As her eyes rested upon Chief's, he let out a single tear drop, the first one he ever had during a live of military training, combat, murder and death.

"John…", she began, with a weak voice.

"Dr….Dr. Halsen… this is… impossible… you… on Reach…" John's voice failed, and he turned to Commander Naxos, as though as to avoid Dr. Halsen's eyes.

"I am sure you have plenty of questions that need to be answered. Much has changed since we lost trace of you. At the time I was no more than a mere Sergeant ,of course", Naxos said.

Chief pondered upon what to question about, but then he remember it was imperative that what happened during his absence was explained. Halo, the Flood, the Pillar of Autumn crew… 

"I appreciate the offer, but…I feel like I should first need to-", but Naxos held up is hand and interrupted him.

"There is no need to tell us. Cortana told us everything about.. Halo, the Forerunner planet. We also know about the Flood. I believe the specimen found in Master Chief's ship is safely isolated?", he asked Dr. Halsen, who was still looking at John as though as he was her son found after long years of desperation.

"Yes, yes.. the Flood has been sealed in Quarantine Lab 04. although dead, tissue samples will be taken for later analysis. We except to find how they manage to mutate their hosts."

"Good, I'll want to hear the results. Now, Chief… you probably want to know what the current situation is," Chief nodded, "so I'll be brutally honest: we're losing.  The whole Covenant fleet arrived at Earth 6 years ago, 1 year after the attack on Reach. We couldn't be any more surprised. The outer defences and colonies held them out for at least an year, but in the end they were all occupied or destroyed. Since then, Earth is under siege. But the Covenant don't want to bombard the planet into glass. They've been trying to gain control of it, and I can say that's the only reason we've resisted for so long."

Chief's memories turned towards the strange room in Reach, resembling Halo's control center, where he found a strange artefact. The Covenant only destroyed the planet after the artefact was destroyed. Could there be a similar room on Earth? What kept the Covenant from razing it?

"We've been able to send in some reinforcements through the siege, but our own outer defences have proven to b more than a challenge for our Armada. And that's where the SPARTAN-III program appeared." Naxos waved his hand towards Kreysha, now looking even moodier than ever.

"With Dr. Halsen's help, we tried to create a new generation of genetically-enhanced soldier, only this time they were created artificially using your- I mean, the SPARTAN-II's DNA."

Chief was completely taken aback by this information. He did not know what to say. Slowly, he looked from Naxos to Kreysha, who turned her back to the to avoid eye contact with him, and from her to Dr. Halsen, who was on the verge of tears.

"Most subjects died at birth, but…our success was imperative! The future of mankind was at stake! I'm sure you understand! John..", she spoke, almost pleadingly.

"Oh, of course he understands!" Replied Mendez lively. "I would have given my own DNA, if they thought they could make anything out of it!" He finished, with a small laugh.

Chief was not sure what so think… but he looked at Kreysha in a whole different way.. she was, in a way, a part of him.

Naxos coughed and continued to speak, as though as to divert Chief's attention from that particular subject. "Unfortunately, the project wasn't as successful as we thought it was. The results achieved by the SPARTAN-III weren't as remotely as good as the one's achieved by their predecessors, but they were still better than what most Marines could achieve. That combined with Mendez' training and an enhanced version of the MJOLNIR armour wore by you made them the best of the best among our ranks, still. Their objective was to board the Covenant flagship and set it to auto-destruct. The explosion would be big enough to breach the Covenant siege, allowing for the UNSC armada to strike it full-force, and possibly defeat it using our own version of the Covenant plasma weapons."

"But that mission was a failure as well?" inquired Chief.

"Indeed it was. All SPARTANS were killed during the mission. Only Kreysha managed to escape alive."

"You abandoned your brothers to death?" Chief was not at all pleased to hear that, because he had always been taught that no soldier should be left behind.

Kreysha's face turned red as Chief asked this with a grave tone in his voice. "Don't you lecture me now! You don't know what it was like!" We.. we were almost getting to the main Engine Room, where he would place the explosive, when this… this Covenant creature appeared out of nowhere, escorted by Elites wielding Plasma swords."

"And? What happened? Elites shouldn't be able to overwhelm a squad of SPARTANS, no matter what weapons they wield."

"That would normally be correct", interrupted Naxos, before Kreysha could reply, "But what has intrigued us is the other creature Kreysha met. From the video footage we got and the description made by her, we assume that is it one of the Covenant religious leaders, probably the one commanding the attack on Earth." 

"And what did it do, this…creature you mention?", Chief asked Kreysha.

"She spoke in this foreign tongue.. I couldn't understand what it was but I was taken by a sudden horror, an inhuman fear I couldn't explain. And then.. the Elites slaughtered my companions, right before my eyes. They couldn't speak, but their faces were horror-struck. Then the… thing looked at me, and I heard his voice inside my head. This time speaking in English. Told me to tell my leaders to give up and surrender the planet.. And then, it.. it...", but her voice died, and she spoke no more.

"So… let me venture a hard guess…You want me to go there and try to do what they failed to?" Chief simply put.

"We don't 'want' you to do anything, Chief.", stated Naxos. "But this is the only way to ever aid the forces on Earth with  large convoys of reinforcements and supplies. It's your call."

Chief looked at each one of them, giving a longer look at Dr. Halsen, as though as he wanted to read her thoughts and council. The choice was clear. He had to do whatever was necessary. For her. For Earth.

"Ok, tell me when."

"As soon as it takes to gather the resources."

"I work alone. Reduces the risk of friendly fire to zero", he finished with a chuckle.

"Don't be a fool, kid!" Spoke Mendez hotly. "Have you forgot everything I taught you? You couldn't pull this off on your own. That's why I'm coming with you."

Chief meant to spoke against this, but as he met his eyes and saw the determination that lay within them, he merely nodded.

Kreysha stepped forward, with a determined look in her face. "And I'm coming with you, too! I know my way around that ship. You'll need me!" 

Chief sighed deeply. He was not used to have an old veteran and a clone "daughter" as war partners, but looking at both of them made him sure he had no other choice.

"Fine, fine, you may come too!" He lowered his voice to a much more friendly tone. "What about you, Cortana? You're free to do whatever you want to."

"Don't even _think _about leaving me behind." Chief smiled.

"Looks as though as the party's all set. You'll be accompanied by a small squad of Helljumpers, I'm going to put you in charge of them." Said Naxos. You'll be leaving as soon as preparations for the operations are done. Don't  expect to leave in less than a week. Oh, and Chief...", he lowered his voice, "Thanks, son. This is a task only the bravest would undertake." He regained his strong voice. "You, soldier!" He called one of the passing soldiers. "Take Master Chief to the armory. Make sure he gets some proper MJOLNIR armour, and give him a new gun. He'll need it."

"Yes, sir! Follow me, Chief."

With a last look at everyone, Chief left the room. Soon… soon he'd have his chance to do something for Mankind… or he would die trying. Either way, he would die with the feeling of having accomplished the purpose for which he had been created. And he was happy for that. Trigger-happy.


End file.
